6CJ9

Crystal structure of lectin from Dioclea lasiophylla seeds (DlyL) complexed with X-Man


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Crystal structure of DlyL, a mannose-specific lectin from Dioclea lasiophylla Mart. Ex Benth seeds that display cytotoxic effects against C6 glioma cells.

Leal, R.B.Pinto-Junior, V.R.Osterne, V.J.S.Wolin, I.A.V.Nascimento, A.P.M.Neco, A.H.B.Araripe, D.A.Welter, P.G.Neto, C.C.Correia, J.L.A.Rocha, C.R.C.Nascimento, K.S.Cavada, B.S.

(2018) Int J Biol Macromol 114: 64-76


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LectinA237Dioclea lasiophyllaMutation(s): 0 
UniProt
Find proteins for C0HK27 (Dioclea lasiophylla)
Explore C0HK27 
Go to UniProtKB:  C0HK27
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XMM (Subject of Investigation/LOI)
Query on XMM

Download Ideal Coordinates CCD File 
D [auth A]5-bromo-4-chloro-1H-indol-3-yl alpha-D-mannopyranoside
C14 H15 Br Cl N O6
OPIFSICVWOWJMJ-HAAGFXOZSA-N
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
C [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
B [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.185 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 64.1α = 90
b = 86.93β = 90
c = 92.82γ = 90
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
iMOSFLMdata reduction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-07
    Type: Initial release
  • Version 1.1: 2018-04-04
    Changes: Data collection, Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Derived calculations, Structure summary